Human Gene CALCOCO2 (uc010wlp.3) Description and Page Index
  Description: Homo sapiens calcium binding and coiled-coil domain 2 (CALCOCO2), transcript variant 2, mRNA.
RefSeq Summary (NM_001261391): This gene encodes a coiled-coil domain-containing protein. The encoded protein functions as a receptor for ubiquitin-coated bacteria and plays an important role in innate immunity by mediating macroautophagy. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, May 2012].
Transcript (Including UTRs)
   Position: hg19 chr17:46,908,350-46,942,607 Size: 34,258 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg19 chr17:46,919,070-46,940,367 Size: 21,298 Coding Exon Count: 13 

Page IndexSequence and LinksGenetic AssociationsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:46,908,350-46,942,607)mRNA (may differ from genome)Protein (467 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsH-INV
HGNCLynxMGIOMIMPubMedStanford SOURCE
UniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CALCOCO2
CDC HuGE Published Literature: CALCOCO2
Positive Disease Associations: Neuroblastoma
Related Studies:
  1. Neuroblastoma
    , , . [PubMed 0]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 40.78 RPKM in Adipose - Subcutaneous
Total median expression: 1175.85 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -31.52101-0.312 Picture PostScript Text
3' UTR -654.712240-0.292 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR012852 - CoCoA

Pfam Domains:
PF07888 - Calcium binding and coiled-coil domain (CALCOCO1) like

ModBase Predicted Comparative 3D Structure on E9PBE5
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AK293329 - Homo sapiens cDNA FLJ51790 complete cds, highly similar to Homo sapiens nuclear domain 10 protein (NDP52), mRNA.
AK314796 - Homo sapiens cDNA, FLJ95668, highly similar to Homo sapiens nuclear domain 10 protein (NDP52), mRNA.
AK303313 - Homo sapiens cDNA FLJ52379 complete cds, highly similar to Homo sapiens nuclear domain 10 protein (NDP52), mRNA.
AK293137 - Homo sapiens cDNA FLJ50435 complete cds, highly similar to Homo sapiens nuclear domain 10 protein (NDP52), mRNA.
AK304024 - Homo sapiens cDNA FLJ55292 complete cds, highly similar to Homo sapiens nuclear domain 10 protein (NDP52), mRNA.
U22897 - Homo sapiens nuclear domain 10 protein (ndp52) mRNA, complete cds.
AK222666 - Homo sapiens mRNA for nuclear domain 10 protein variant, clone: CBR02087.
AK298177 - Homo sapiens cDNA FLJ55141 complete cds, highly similar to Homo sapiens nuclear domain 10 protein (NDP52), mRNA.
AK223227 - Homo sapiens mRNA for nuclear domain 10 protein variant, clone: STM01975.
BC004130 - Homo sapiens calcium binding and coiled-coil domain 2, mRNA (cDNA clone MGC:1399 IMAGE:3505988), complete cds.
BC015893 - Homo sapiens calcium binding and coiled-coil domain 2, mRNA (cDNA clone MGC:17318 IMAGE:3921397), complete cds.
AB527571 - Synthetic construct DNA, clone: pF1KB6650, Homo sapiens CALCOCO2 gene for calcium binding and coiled-coil domain 2, without stop codon, in Flexi system.
CU677493 - Synthetic construct Homo sapiens gateway clone IMAGE:100017287 5' read CALCOCO2 mRNA.
HQ448259 - Synthetic construct Homo sapiens clone IMAGE:100071661; CCSB000279_03 calcium binding and coiled-coil domain 2 (CALCOCO2) gene, encodes complete protein.
JF432510 - Synthetic construct Homo sapiens clone IMAGE:100073731 calcium binding and coiled-coil domain 2 (CALCOCO2) gene, encodes complete protein.
KJ892973 - Synthetic construct Homo sapiens clone ccsbBroadEn_02367 CALCOCO2 gene, encodes complete protein.
KJ898182 - Synthetic construct Homo sapiens clone ccsbBroadEn_07576 CALCOCO2 gene, encodes complete protein.
CR456763 - Homo sapiens full open reading frame cDNA clone RZPDo834D034D for gene NDP52, nuclear domain 10 protein; complete cds, incl. stopcodon.
AK310648 - Homo sapiens cDNA, FLJ17690.
LF349779 - JP 2014500723-A/157282: Polycomb-Associated Non-Coding RNAs.
AF085965 - Homo sapiens full length insert cDNA clone YS16F09.
JD157045 - Sequence 138069 from Patent EP1572962.
JD404909 - Sequence 385933 from Patent EP1572962.
JD082619 - Sequence 63643 from Patent EP1572962.
JD308377 - Sequence 289401 from Patent EP1572962.
JD524889 - Sequence 505913 from Patent EP1572962.
JD046563 - Sequence 27587 from Patent EP1572962.
JD232305 - Sequence 213329 from Patent EP1572962.
JD446920 - Sequence 427944 from Patent EP1572962.
JD172274 - Sequence 153298 from Patent EP1572962.
JD536378 - Sequence 517402 from Patent EP1572962.
JD560308 - Sequence 541332 from Patent EP1572962.
JD090754 - Sequence 71778 from Patent EP1572962.
JD086778 - Sequence 67802 from Patent EP1572962.
JD298647 - Sequence 279671 from Patent EP1572962.
JD221209 - Sequence 202233 from Patent EP1572962.
JD315496 - Sequence 296520 from Patent EP1572962.
JD158644 - Sequence 139668 from Patent EP1572962.
JD051633 - Sequence 32657 from Patent EP1572962.
JD418826 - Sequence 399850 from Patent EP1572962.
JD418923 - Sequence 399947 from Patent EP1572962.
JD259710 - Sequence 240734 from Patent EP1572962.
JD153071 - Sequence 134095 from Patent EP1572962.
JD160916 - Sequence 141940 from Patent EP1572962.
JD492085 - Sequence 473109 from Patent EP1572962.
JD513654 - Sequence 494678 from Patent EP1572962.
JD054072 - Sequence 35096 from Patent EP1572962.
JD388955 - Sequence 369979 from Patent EP1572962.
JD109610 - Sequence 90634 from Patent EP1572962.
JD501186 - Sequence 482210 from Patent EP1572962.
JD265183 - Sequence 246207 from Patent EP1572962.
JD173991 - Sequence 155015 from Patent EP1572962.
JD489114 - Sequence 470138 from Patent EP1572962.
JD032275 - Sequence 13299 from Patent EP1572962.
JD238986 - Sequence 220010 from Patent EP1572962.
JD255565 - Sequence 236589 from Patent EP1572962.
JD541466 - Sequence 522490 from Patent EP1572962.
JD143871 - Sequence 124895 from Patent EP1572962.
JD267708 - Sequence 248732 from Patent EP1572962.
JD069433 - Sequence 50457 from Patent EP1572962.
JD081647 - Sequence 62671 from Patent EP1572962.
JD207528 - Sequence 188552 from Patent EP1572962.
JD504436 - Sequence 485460 from Patent EP1572962.
JD098400 - Sequence 79424 from Patent EP1572962.
MA585356 - JP 2018138019-A/157282: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: E9PBE5, E9PBE5_HUMAN, NM_001261391, NP_001248324, uc010wlp.2
UCSC ID: uc010wlp.3
RefSeq Accession: NM_001261391
Protein: E9PBE5 CCDS: CCDS11538.1, CCDS58558.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001261391.1
exon count: 14CDS single in 3' UTR: no RNA size: 3745
ORF size: 1404CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3008.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.